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onemap (version 2.1.3)

Construction of Genetic Maps in Experimental Crosses: Full-Sib, RILs, F2 and Backcrosses

Description

Analysis of molecular marker data from model (backcrosses, F2 and recombinant inbred lines) and non-model systems (i. e. outcrossing species). For the later, it allows statistical analysis by simultaneously estimating linkage and linkage phases (genetic map construction) according to Wu et al. (2002) . All analysis are based on multipoint approaches using hidden Markov models.

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Install

install.packages('onemap')

Monthly Downloads

662

Version

2.1.3

License

GPL-3

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Repository

https://github.com/augusto-garcia/onemap

Maintainer

Cristiane Taniguti

Last Published

February 17th, 2020

Functions in onemap (2.1.3)

Creates a new sequence by adding markers.

onemap_example_bc

Simulated data from a backcross population

OneMap interface with MDSMap package with possibilitie of multipoint distances estimation

Read data from a Mapmaker raw file

test_segregation

test_segregation

Assign markers to preexisting linkage groups

test_segregation_of_a_marker

test_segregation_of_a_marker

Mapping functions Haldane and Kosambi

Construct the linkage map for a sequence of markers

Informs the segregation patterns of markers

Search for the best order of markers combining compare and try_seq functions

onemap-internal

Internal onemap functions

Read data from all types of progenies supported by OneMap

Data generated from VCF file with biallelic markers from a f2 intercross population

Draw a graphic of raw data for any OneMap population

print.onemap_segreg_test

Show the results of segregation tests

Print method for object class 'rf_2pts'

Show markers with/without segregation distortion

Create a sequence of markers

mapmaker_example_bc

Simulated data from a backcross population

onemap_read_vcfR

Convert vcfR object to onemap object

Suggests a LOD Score for two point tests

onemap_example_riself

Simulated data from a RIL population produced by selfing.

Recombination Counting and Ordering

Defines the default mapping function

vcf_example_out

Data generated from VCF file with biallelic markers from a full-sib family derived from two outbred parents

plot_by_segreg_type

Draw a graphic showing the number of markers of each segregation pattern.

plot.onemap_segreg_test

Plot p-values for chi-square tests of expected segregation

Two-point analysis between genetic markers

Convert variants from a VCF file to OneMap file format

mapmaker_example_f2

Simulated data from a F2 population

Assign markers to linkage groups

Allocate markers into bins

Show the results of grouping procedure

Data generated from VCF file with biallelic markers from a f2 backcross population

print.group_seq

Show the results of grouping markers to preexisting sequence

Plots pairwise recombination fractions and LOD Scores in a heatmap

Compares and displays plausible alternative orders for a given linkage group

Rapid Chain Delineation

onemap_example_out

Data from a full-sib family derived from two outbred parents

vcf_example_riself

Data generated from VCF file with biallelic markers from a RIL population produced by selfing

onemap_example_f2

Simulated data from a F2 population

Try to map a marker into every possible position between markers in a given map

Unidirectional Growth

Print method for object class 'try'

write_onemap_raw

Convert onemap object to onemap raw file

Write a genetic map to a file

create_data_bins

New dataset based on bins

Bonferroni_alpha

Calculates individual significance level to be used to achieve a global alpha (with Bonferroni)

Creates a new sequence by dropping markers.

Draw a linkage map

Combine OneMap datasets

Draw a genetic map

est_map_hmm_out

C++ routine for multipoint analysis in outcrossing populations

Compare all possible orders (exhaustive search) for a given sequence of markers

create_dataframe_for_plot_outcross

Create a dataframe suitable for a ggplot2 graphic